Identification of hepatotoxin-producing cyanobacteria by DNA-chip

Environmental Microbiology

Volumn 10, Issue 3, 2008, Pages 653-664

  Rantala, Anne ^a   Rizzi, Ermanno ^b   Castiglioni, Bianca ^b   De Bellis, Gianluca ^b   Sivonen, Kaarina ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; BACTERIAL TOXIN; CYCLOPEPTIDE; FRESH WATER; MICROCYSTIN; NODULARIN;

ARTICLE; BACTERIUM IDENTIFICATION; BIOSYNTHESIS; CYANOBACTERIUM; DNA FINGERPRINTING; DNA MICROARRAY; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; POLYMERASE CHAIN REACTION;

BACTERIAL PROTEINS; BACTERIAL TOXINS; BACTERIAL TYPING TECHNIQUES; CYANOBACTERIA; DNA FINGERPRINTING; DNA, BACTERIAL; ECOSYSTEM; FRESH WATER; MICROCYSTINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEPTIDES, CYCLIC; POLYMERASE CHAIN REACTION;

ANABAENA; CYANOBACTERIA; MICROCYSTIS; NODULARIA; NOSTOC; PLANKTOTHRIX;

EID: 38549100519     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01488.x     Document Type: Article

References (43)

1. Bodrossy, L. Sessitsch, A. (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7 : 245 254.
2. Castiglioni, B., Rizzi, E., Frosini, A., Sivonen, K., Rajaniemi, P., Rantala, A., et al. (2004) Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol 70 : 7161 7172.
3. Chen, J., Iannone, M.A., Li, M.-S., Taylor, J.D., Rivers, P., Nelsen, A.J., et al. (2000) A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 10 : 549 557.
4. Christiansen, G., Fastner, J., Erhard, M., Börner, T. Dittmann, E. (2003) Microcystin biosynthesis in Planktothrix: genes, evolution, and manipulation. J Bacteriol 185 : 564 572.
5. Christiansen, G., Kurmayer, R., Liu, Q. Börner, T. (2006) Transposons inactivate biosynthesis of the nonribosomal peptide microcystin in naturally occurring Planktothrix spp. Appl Environ Microbiol 72 : 117 123.
6. Consolandi, C., Busti, E., Pera, C., Delfino, L., Ferrara, G.B., Bordoni, R., et al. (2003) Detection of HLA polymorphisms by ligase detection reaction and a universal array format: a pilot study for low resolution genotyping. Hum Immunol 64 : 168 178.
7. Dittmann, E. Börner, T. (2005) Genetic contributions to the risk assessment of microcystin in the environment. Toxicol Appl Pharmacol 203 : 192 200.
8. Dittmann, E., Neilan, B.A., Erhard, M., von Döhren, H. Börner, T. (1997) Insertional mutagenesis of a peptide synthetase gene that is responsible for hepatotoxin production in the cyanobacterium Microcystis aeruginosa PCC 7806. Mol Microbiol 26 : 779 787.
9. Favis, R., Day, J.P., Gerry, N.P., Phelan, C., Narod, S. Barany, F. (2000) Universal DNA array detection of small insertions and deletions in BRCA1 and Brca2. Nat Biotechnol 18 : 561 564.
10. Fouquet, C., Antoine, M., Tisserand, P., Favis, R., Wislez, M., Commo, F., et al. (2004) Rapid and sensitive p53 alteration analysis in biopsies from lung cancer patients using a functional assay and a universal oligonucleotide array: a prospective study. Clin Cancer Res 10 : 3479 3489.
11. Gerry, N.P., Witowski, N.E., Day, J., Hammer, R.P., Barany, G. Barany, F. (1999) Universal DNA microarray method for multiplex detection of low abundance point mutations. J Mol Biol 292 : 251 262.
12. Giovannoni, S.J., DeLong, E.F., Schmidt, T.M. Pace, N.R. (1990) Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl Environ Microbiol 56 : 2572 2575.
13. Gugger, M., Lyra, C., Henriksen, P., Couté, A., Humbert, J.-F. Sivonen, K. (2002) Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon. Int J Syst Evol Microbiol 52 : 1867 1880.
14. Hisbergues, M., Christiansen, G., Rouhiainen, L., Sivonen, K. Börner, T. (2003) PCR-based identification of microcystin-producing genotypes of different cyanobacterial genera. Arch Microbiol 180 : 402 410.
15. Jungblut, A.-D. Neilan, B.A. (2006) Molecular identification and evolution of the cyclic peptide hepatotoxins, microcystin and nodularin, synthetase genes in three orders of cyanobacteria. Arch Microbiol 185 : 107 114.
16. Kellmann, R., Mills, T. Neilan, B.A. (2006) Functional modeling and phylogenetic distribution of putative cylindrospermopsin biosynthesis enzymes. J Mol Evol 62 : 267 280.
17. Koskenniemi, K., Lyra, C., Rajaniemi-Wacklin, P., Jokela, J. Sivonen, K. (2007) A quantitative real-time PCR detection of toxic Nodularia cyanobacteria in the Baltic Sea. Appl Environ Microbiol 73 : 2173 2179.
18. Kurmayer, R., Christiansen, G., Fastner, J. Börner, T. (2004) Abundance of active and inactive microcystin genotypes in populations of the toxic cyanobacterium Planktothrix spp. Environ Microbiol 6 : 831 841.
19. Kurmayer, R. Gumpenberger, M. (2006) Diversity of microcystin genotypes among populations of the filamentous cyanobacteria Planktothrix rubescens and Planktothrix agardhii. Mol Ecol 15 : 3849 3861.
20. Long, W.-H., Xiao, H.-S., Gu, X.-M., Zhang, Q.-H., Yang, H.-J., Zhao, G.-P. Liu, J.-H. (2004) A universal microarray for detection of SARS coronavirus. J Virol Methods 121 : 57 63.
21. Loy, A. Bodrossy, L. (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363 : 106 119.
22. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar., et al. (2004) arb: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
23. Lyra, C., Suomalainen, S., Gugger, M., Vezie, C., Sundman, P., Paulin, L. Sivonen, K. (2001) Molecular characterization of planktic cyanobacteria of Anabaena, Aphanizomenon, Microcystis and Planktothrix genera. Int J Syst Evol Microbiol 51 : 513 526.
24. Matsunaga, T., Nakayama, H., Okochi, M. Takeyama, H. (2001) Fluorescent detection of cyanobacterial DNA using bacterial magnetic particles on a MAG-microarray. Biotechnol Bioeng 73 : 400 405.
25. Mikalsen, B., Boison, G., Skulberg, O.M., Fastner, J., Davies, W., Gabrielsen, T.M., et al. (2003) Natural variation in the microcystin synthetase operon mcyABC and impact on microcystin production in Microcystis strains. J Bacteriol 185 : 2774 2785.
26. Moffitt, M.C. Neilan, B.A. (2004) Characterization of the nodularin synthetase gene cluster and proposed theory of the evolution of cyanobacterial hepatotoxins. Appl Environ Microbiol 70 : 6353 6362.
27. Neilan, B.A., Jacobs, D., del Dot, T., Blackall, L.L., Hawkins, P.R., Cox, P.T. Goodman, A.E. (1997) rRNA sequences and evolutionary relationships among toxic and nontoxic cyanobacteria of the genus Microcystis. Int J Syst Bacteriol 47 : 693 697.
28. Nishizawa, T., Ueda, A., Asayama, M., Fujii, K., Harada, K.-I., Ochi, K. Shirai, M. (2000) Polyketide synthase gene coupled to the peptide synthetase module involved in the biosynthesis of the cyclic heptapeptide microcystin. J Biochem 127 : 779 789.
29. Qin, S., Zhao, X., Pan, Y., Liu, J., Feng, G., Fu, J., et al. (2005) An association study of the N-methyl-d-aspartate reseptor NR1 subunit gene (GRIN1) and NR2B subunit gene (GRIN2B) in schizophrenia with universal DNA microarray. Eur J Hum Genet 13 : 807 814.
30. Rajaniemi-Wacklin, P., Rantala, A., Kuuppo, P., Haukka, K. Sivonen, K. (2007) Cyanobacterial community composition in shallow, eutrophic Lake Tuusulanjärvi studied by microscopy, strain isolation, DGGE and cloning. Algol Studies in press).
31. Rantala, A., Fewer, D.P., Hisbergues, M., Rouhiainen, L., Vaitomaa, J., Börner, T. Sivonen, K. (2004) Phylogenetic evidence for the early evolution of microcystin synthesis. Proc Nat Acad Sci USA 101 : 568 573.
32. Rantala, A., Rajaniemi-Wacklin, P., Lyra, C., Lepistö, L., Rintala, J., Mankiewicz-Boczek, J. Sivonen, K. (2006) Detection of microcystin-producing cyanobacteria in Finnish lakes with genus-specific microcystin synthetase gene E (mcyE) PCR and associations with environmental factors. Appl Environ Microbiol 72 : 6101 6110.
33. Rouhiainen, L., Vakkilainen, T., Siemer, B.L., Buikema, W., Haselkorn, R. Sivonen, K. (2004) Genes coding for hepatotoxic heptapeptides (microcystins) in the cyanobacterium Anabaena strain 90. Appl Environ Microbiol 70 : 686 692.
34. Rudi, K., Skulberg, O.M., Skulberg, R. Jakobsen, K.S. (2000) Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl Environ Microbiol 66 : 4004 4011.
35. Saitou, N. Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
36. Sivonen, K. Jones, G. (1999) Cyanobacterial toxins. In Toxic Cyanobacteria in Water: A Guide to Their Public Health Consequences, Monitoring, and Management. Chorus, I. Bartram, J. (eds). London, UK : E & FN Spon, pp. 41 111.
37. Thompson, J.D., Higgins, D.G. Gibson, T.J. (1994) clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 : 4673 4680.
38. Tillett, D., Dittmann, E., Erhard, M., von Döhren, H., Börner, T. Neilan, B.A. (2000) Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: an integrated peptide-polyketide synthetase system. Chem Biol 7 : 753 764.
39. Tillett, D., Parker, D.L. Neilan, B.A. (2001) Detection of toxigenicity by a probe for the microcystin synthetase A gene (mcyA) of the cyanobacterial genus Microcystis: comparison of toxicities with 16S rRNA and phycocyanin operon (phycocyanin intergenic spacer) phylogenies. Appl Environ Microbiol 67 : 2810 2818.
40. Vaitomaa, J., Rantala, A., Halinen, K., Rouhiainen, L., Tallberg, P., Mokelke, L. Sivonen, K. (2003) Quantitative real-time PCR for determination of microcystin synthetase gene E copy numbers for Microcystis and Anabaena in lakes. Appl Environ Microbiol 69 : 7289 7297.
41. Vezie, C., Brent, L., Sivonen, K., Bertru, G., Lefeuvre, J.-C. Salkinoja-Salonen, M. (1998) Variation of microcystin content of cyanobacterial blooms and isolated strains in Lake Grand-Lieu (France). Microb Ecol 35 : 126 135.
42. Via-Ordorika, L., Fastner, J., Kurmayer, R., Hisbergues, M., Dittmann, E., Komarek, J., et al. (2004) Distribution of microcystin-producing and non-microcystin-producing Microcystis sp. in European freshwater bodies: detection of microcystins and microcystin genes in individual colonies. Syst Appl Microbiol 27 : 592 602.
43. Zhou, J. Thompson, D.K. (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13 : 204 207.